Genetic Editing of Ideal Small Grain Size Genes Enables Fully Mechanized Hybrid Rice Breeding

Jun 04, 2024

By Zhang Nannan

In a study published in Nature Plants, Prof. Li Yunhai from the Institute of Genetics and Developmental Biology (IGDB) of the Chinese Academy of Sciences and Profs. Zhu Xudong and Wang Yuexing from the China National Rice Research Institute have identified an ideal small grain size gene, GSE3.

They demonstrated that fully mechanized hybrid seed production and increased seed number can be achieved using small-grain alleles of GSE3 in male sterile lines.

Crop hybrid technologies have contributed to significant yield improvements worldwide. Rice yield has increased by 20%–30% over the past few decades through the use of hybrid rice, enhancing food security. At present, labor-intensive manual steps in F1 hybrid seed production hinder full mechanization in hybrid rice breeding.

A promising approach to achieving this goal is to develop small-grain male sterile lines and large-grain restorer lines that allow mechanical separation of small F1 hybrid seeds from mixed plantings of these two lines by using a simple sifter. An ideal small-grain male sterile line should also have minimal negative effects on F1 hybrid seed number and hybrid rice yield in field trials.

Tianyouhuazhan (TYHZ) is an elite hybrid rice variety that has been widely grown in China for decades. Tianfeng A (TFA), Tianfeng B (TFB), and Huazhan (HZ) are male sterile, maintainer, and restorer lines of TYHZ, respectively. The researchers crossed TFB with various small-grain rice varieties and successfully bred an ideal small-grain maintainer line Xiaoqiao B (XQB) and its corresponding new male sterile line, Xiaoqiao A (XQA).

In addition, a large-grain indica variety Kuangsijiadi was crossed with the restorer line HZ to create the large-grain restorer line Da Huazhan (DHZ). Field trials showed that the male sterile restorer combination XQA-DHZ enabled fully mechanized hybrid rice production, increased hybrid seed number, and did not affect hybrid rice yield.

The researchers identified that the GSE3 gene is responsible for the small-grain phenotype in XQA and XQB. Concurrently, they performed a large-scale mutagenesis screen to identify genes for breeding ideal small-grain male sterile lines and isolated m238, a mutant with small grains and an increased grain number without compromising other agronomic traits. Further analysis revealed that m238 was a new allele of GSE3.

Moreover, they performed genome editing of the GSE3 gene in three- and two-line hybrid rice systems using CRISPR-Cas9 technology, resulting in fully mechanized hybrid seed production and considerably increased hybrid seed number. They also found that GSE3 encodes a GCN5-related N-acetyltransferase-like protein that affects histone acetylation levels.

GSE3 is recruited by the transcription factor GS2 to the promoters of its co-regulated grain size genes and influences the histone acetylation status of its co-regulated genes, thereby regulating grain size.

This study elucidates that mechanized hybrid seed production can be achieved for some elite hybrid rice varieties only by editing the GSE3 gene in male sterile lines when the grain thickness difference between the restorer lines and the male sterile lines is relatively large.

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Video: Turning Plant Defense Into a Management Strategy

Turning Plant Defense Into a Management Strategy

Understanding how a plant responds to stress is one thing.

Using that knowledge to make better management decisions is another.

Systemic acquired resistance, or SAR, is the plant's more direct defense response. When stress or infection occurs, the plant begins signaling throughout its system and preparing defensive compounds.

But if we know that response exists, can we help prepare the plant before the stress arrives?

The answer starts with understanding what triggers the response and what the plant needs to carry it out.

The Trigger and the Fuel

Salicylic acid plays an important role in triggering the SAR pathway.

Think of it as turning the truck on.

The engine may be running, but it still needs fuel to do the work.

In this case, manganese plays an important role in supporting the enzyme systems involved in the plant's defensive response.

This makes manganese status an important part of the conversation. Whether a producer is using tissue testing, sap analysis, or simply scouting for visible deficiency symptoms, the goal is to make sure the plant has adequate manganese available.

Manganese is required in relatively small amounts, but that does not make its role small.

If the plant receives a signal to defend itself but lacks the nutrition needed to support that response, it may struggle to carry out the process efficiently.

The trigger matters.

The fuel matters too.

Prepare Before the Stress Arrives

The best time to think about stress management is before the plant is overwhelmed.

Once a crop is already struggling, management can quickly turn into a game of catch-up.

This is similar to nitrogen management. Once a plant becomes severely deficient, correcting the problem does not necessarily erase the time and yield potential already lost.

Plant defense can work the same way.

Low-rate, targeted approaches designed to support the SAR pathway may fit best ahead of an expected stress event rather than after significant damage has already occurred.

That requires producers to think about predictable stress.

We may not know exactly what the weather will do tomorrow, but we generally know summer heat is coming. We know certain field conditions increase disease pressure. We know a herbicide application can temporarily stress a crop as the plant processes the chemistry.

Even a properly timed and labeled herbicide application can create a temporary response in the plant.

That does not mean the herbicide is bad.

Weeds can create significantly more yield loss than the temporary stress caused by controlling them.

The question is not whether we should eliminate every stressor.

The question is whether we can better prepare the plant to manage necessary and predictable stress.

Not All Stress Is Bad

Stress is a normal part of plant growth.

A perfectly stress-free environment does not exist in the field.

In fact, some stress is necessary for normal plant development. A plant responds to wind, temperature, moisture, sunlight, and countless other environmental signals throughout the season.

The environment is stress.

The plant's job is to manage it.

Problems begin when the stress load becomes greater than the plant's ability to respond.

Extreme heat, drought, high salt concentrations, disease pressure, and even certain management practices can add to that load.

This is where understanding SAR becomes useful.

Instead of waiting until the plant is visibly struggling, producers can begin identifying periods when stress is likely and make management decisions around those windows.

ISR Starts With the Soil

While SAR is a more direct defense response, induced systemic resistance, or ISR, brings the conversation back to soil health.

The longevity of a farm is closely connected to the health of its soil.

Carbon plays a major role because it supports biological life within the soil. Bacteria, fungi, and other organisms interact with plant roots and influence how the plant grows, accesses nutrients, and prepares for stress.

This is why soil health cannot be reduced to one product or one application.

It is a system.

Keeping living plants in the field longer can support biological activity. Cover crops may fit some operations. Better water management can improve soil conditions.